I was finally able to get back to my White Water this weekend. Of course, my primary goal is still to get the DMD controller back into working state. I just picked up the controller and some tools and took it back here with me
Here's the approach I'm taking now.
On the left, there is a broken White Water's controller and on the right the Star treks, that is all fine and dandy.
I measured the resistance of all the components and all the traces on both boards and try to identify any suspicious components, that might be causing too high negative voltages.
Anyway, the following measured quite different than on the working board: D4, D5 and D7 diodes. Q4, Q5 and Q6 transistors and R3, R4 and R6 resistors. These are the things I'll replace.
I guess I'm going shopping tomorrow. Naturally I will report about the results.